Fine-Tuning Sample Preparation Techniques

Producing High-Quality Data through the Optimization of DNA and RNA Extraction

Researchers at the Emory University School of Medicine are using Applied Biosystems' MagMax 96 Express Instrument for RNA extraction.

The push toward personalized medicine and the compression of the drug development pipeline puts more pressure than ever on the genome space. At CHI’s “Genomics Tools & Technologies” meeting to be held in June, the ever-changing and challenging issues around extracting, creating, and keeping samples and templates of highest quality will be addressed, as this is the key factor for producing high-throughput data of optimal quality.

“There are quite a few challenges,” comments Austin Tanney, Ph.D., scientific liaison manager, Almac Diagnostics . “But there are a number of really good reasons to work in this space, one of the chief reasons being what this can mean for personalized medicine.”

FFPE Tissue

FFPE tissues will be a hot topic at this conference. “One of the reasons we work with FFPE is that there are literally hundreds of thousands of samples available—a huge amount of information to work with,” says Dr. Tanney. “Doing retrospective studies can cut off years of development time for a diagnostic. What is most important, however, is that if a diagnostic test works from FFPE there is no required change to clinical practice to use this test. This is not a case when the test must be carried out on fresh frozen material.”

Personalized medicine, in this case, using genomics to determine a course of care, is still in its infancy, but advances in technology to enable DNA and RNA extraction are advancing the field. Dr. Tanney’s talk will discuss the ways in which his group has been able to use what they have found in FFPE samples to advance Almac’s cancer studies. “Cancer has always had a one-size-fits-all treatment regimen, even though it’s a heterogeneous disease,” continues Dr. Tanney. “Clearly, this is an area where treatment can be personalized.”

But working with FFPE has its challenges, he notes. “High-quality RNA can easily be reverse transcribed and amplified, and in degraded RNA, use of oligo dT primers can be a limiting step. Getting usable RNA is also a challenge because cross-links get broken—extracting RNA degrades it.”

To meet the challenges of the complexity of working with FFPE tissues in the cancer field, Almac developed Cancer DSA research tools, which are high-density microarrays based on the transcriptome of an individual disease and are capable of obtaining robust data from FFPE samples and delivering additional information on the chosen disease setting.

“One of the biggest issues in developing prognostic and predictive tests is the availability of samples,” points out Dr. Tanney. “Fresh frozen is virtually impossible, but working with FFPE is not easy, either.”

And working with a disease as heterogenous as cancer is akin to trying to hit a moving target. “For example, there are at least five subgroups of breast cancer,” he adds. “That there is such diversity in the disease and not in treatment, means that there has to be better ways of treating cancer than the way we are presently going about it.”

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